Dear Moeed: The simulation has given you CONFOUT.GRO with new [good] density. I guess this is the only output file you really need here. If you want a detailed trajectory, please just use: nstxout = something nstvout = something nstfout = something nstxtcout = something
You may also use g_energy to look at the evolution of the PE density, energies, etc. As for the pbc option, this is just an erratum. You are right. Vitally > Dear Dr. Chaban, > > Thank you for your attention. Actually with the revised mdp file you sent me > and the initial configuration of my 8PE system, I tried to compress the > system. The simulation tales very long and produces nothing. grompp is > giving me: > processing topology... > Analysing residue names: > There are: 240 OTHER residues > There are: 0 PROTEIN residues > There are: 0 DNA residues > Analysing Other... > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 270x250x250, spacing 0.119 0.120 0.120 > This run will generate roughly 2 Mb of data > > Generating 2Mb !!!! This is concerning since I am running NPT for 2ns. > > I just used the mdp file and the only thing I changed was pbc=full. Actually > I tried this option but grompp gave a warning saying that I shoudl use xyz > option. I did not even find "full" optioon in the manual for pbc! I am > wondeig how you could run the simulation with this setting. > > Please help me with this matter. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
